Well, knowing the naming conventions for bones helped a lot with this problem, but still things aren't right. When I paste a flipped pose on the armature I'm working with, it comes out kinda deformed. Arms bend the wrong direction, and stuff like that. I'm kinda wondering if there are any naming conventions for non symmetrical bones, the neck and spine, etc. I don't think that's the problem though. From what I've heard, there's some kind of trick with aligning the axis of the bones in a certain direction (I might have some trouble because I ended up joining two armatures into one maybe?). But I haven't been able to figure out how to fix it, or what I should do differently next time in order to avoid it happening again.

Essentially, I'd like to know everything that could possibly go wrong with the flipped poses, 'cause it's kinda frustrating to have an armature that works fine for everything else except this one feature.

From what I remember and from the little test I did 30 seconds ago, it seems lke Blender flips/mirrors the pose on the ZoY plane. Basicly, the best way to make this work and fit your armature when flipping poses is to setup the armature like this (and I mean the armature object, not the bones).

Z axis: points to the front of the armature
Y axis: points to the top of the armature
X axis: points to the left side of the armature

Basicly, just setup your armature when your character is facing at the screen.

Martin

Life is what happens to you when you're busy making other plans.
- John Lennon

Well, I think that helped a little bit, but a few of the bones just seem to rotate in totally arbitrary directions. The legs are supposed to be direct copies of each other (I even tried deleting one leg, making a new copy from the remaining leg and then renaming all the bones just to be sure) but oddly enough they end up twisted just a bit differently. The joints are all at the exact same locations, but the orientation of the wireframe is different. I figured it was nothing, since it doesn't affect the way the mesh deforms to them, but when I try to copy a pose each leg has a distinctly different rotation. If I bend one of the knees backwards, the other interprets it as bending sideways.
Is there some way of copying two halves of an armature more reliably then? All I know of is the usual scale-x method and that keeps giving me random twists in the bones. Makes no sense....

Edit: It gets even weirder. I just tried deleting one side of the armature and starting over again. If I flip the object itself, the bones stay "normal", but as soon as I join the two objects (the normal and flipped copy) all the bones from the copy spontaneously twist in a different direction. I don't think there's any way to get a perfectly symmetrical armature.

Edit2: Alright, happy but embarassed . Please ignore, I got it figured out now. CTRL+N to recalculate "roll" seems to get things working right.